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Study of the Genetic Variability of Peach in Susceptibility to Brown Rot During Fruit Development in Relation with Changes in Ph

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Study of the Genetic Variability of Peach in Susceptibility to Brown Rot During Fruit Development in Relation with Changes in Ph Study of the genetic variability of peach in susceptibility to brown rot during fruit development in relation with changes in physical and biochemical characteristics of the fruit Leandro de Oliveira Lino To cite this version: Leandro de Oliveira Lino. Study of the genetic variability of peach in susceptibility to brown rot during fruit development in relation with changes in physical and biochemical characteristics of the fruit. Agricultural sciences. Université d’Avignon, 2016. English. NNT : 2016AVIG0677. tel- 01635960 HAL Id: tel-01635960 https://tel.archives-ouvertes.fr/tel-01635960 Submitted on 16 Nov 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ACADEMIE D’AIX-MARSEILLE UNIVERSITE D’AVIGNON ET DES PAYS DE VAUCLUSE THESE Présentée pour obtenir le grade de Docteur en Sciences De l’Université d’Avignon et des Pays de Vaucluse Spécialité : Sciences Agronomiques Etude de la variabilité génétique de la sensibilité à la pourriture brune au cours du développement du fruit chez la pêche en lien avec l’évolution des caractéristiques biochimiques du fruit Par Leandro DE OLIVEIRA LINO Soutenue le 15 novembre 2016 devant un jury composé de : Bruno LE CAM Directeur de recherche INRA, Angers Rapporteur Jean-Luc REGNARD Professeur SupAgro, Montpellier Rapporteur Bénédicte BAKAN Chargée de recherche INRA, Nantes Examinatrice Véronique LEFEBVRE Directrice de Recherche INRA GAFL, Avignon Examinatrice Michel GENARD Directeur de recherche INRA, Avignon Directeur de thèse Bénédicte QUILOT-TURION Chargée de recherche INRA, Avignon Directrice de thèse Encadrement de la thèse : Bénédicte QUILOT-TURION, Michel GENARD Ecole Doctorale : Agrosciences et Sciences, Avignon Laboratoires d’accueil : INRA-UR1052 « Génétique et Amélioration des Fruits et Légumes » INRA-UR1115 « Plantes et Systèmes de culture Horticoles » SOMMAIRE INTRODUCTION GENERALE 1 Contexte de la thèse 3 1.1 Production mondiale et importance de la pêche pour la France et pour le Brésil 3 1.2 Caractéristiques du Pêcher 3 1.3 La Pourriture Brune 4 1.4 Traitement chimique – les conséquences pour la santé humaine et environnement 5 2 Les mécanismes de résistance 7 2.1 Caractéristiques physique potentiellement liées à la résistance constitutive 7 2.2 Caractéristiques biochimiques potentiellement liées à la résistance constitutive 8 2.3 Les mécanismes de résistance induite 9 3 La recherche de sources de résistance 10 4 Présentation de la thèse 11 4.1 Hypothèses 11 4.2 Objectifs de la thèse 11 4.3 Le matériel végétal 12 4.4 Plan de la thèse 12 5 Publications et communications scientifiques 14 5.1 Publications 14 5.2 Communications orales 14 Chapitre 1: Synthèse bibliographique sur la pourriture brune chez les Prunus 18 1 Introduction 19 2 Monilinia spp. fungi cause brown rot 21 2.1 Taxonomy 21 2.2 Differentiation of Monilinia species 21 2.3 Host range and distribution of Monilinia spp. 23 3 Penetration sites in relation to fruit growth 24 3.1 Fruit susceptibility evolves along fruit development 25 3.2 Infection by direct penetration of the cuticle 26 3.3 Infection through the trichomes basis 26 3.4 Infection through stomata 27 3.5 Infection through skin cracks and wounds 27 4 Infection development 29 4.1 Adhesion to the cuticle and germination 29 4.2 Latent infection 29 4.3 Appressorium formation and hypha penetration 30 4.4 Appressoria melanization increase pathogenicity 31 4.5 pH lowering regulates the expression of pathogenicity genes. 31 4.6 Biochemical arsenal of Monilinia spp. 32 4.7 Post-penetration 33 5 Host factors for BR resistance/susceptibility in fruit 34 5.1 Constitutive components of BR resistance: plant cuticle, a multi-component barrier 34 5.2 Phenolic acids and their redox-mediated role in fungal inhibition 36 5.3 Active mechanisms in response to pathogen attack: defence proteins 37 5.4 ROS, oxidative stress and programmed cell death 39 6 Breeding for brown rot (BR) resistance 40 6.1 Genetic resources, breeding programs and phenotyping strategies 40 6.2 Field-borne inoculum assessment 41 6.3 Artificial infection assessment 41 6.4 QTL of resistance 44 7 Conclusion 46 Chapite 2 : Etude de la poailité d’ifetio au ous du développeet du fuit, e lie ave les caractéristiques structurales et biochimiques du fruit 57 1 Introduction 58 2 Material and Methods 61 2.1 Plant material 61 2.2 Fruit sampling 61 2.3 Extraction 62 2.4 Analysis of wax compounds 62 2.5 HPLC Analysis 62 2.6 Cuticular conductance 63 2.7 Monilinia susceptibility 63 2.8 Statistical analysis 64 3 Results 64 3.1 Evolution of fruit characteristics during development 64 3.2 Fruit growth 64 3.3 Fruit surface conductance 65 3.4 Fruit susceptibility to M. laxa 65 3.5 Identification and characterization of fruit cuticular compounds 65 3.6 Cuticular wax composition 66 3.7 Identification of secondary compounds 66 3.8 Developmental variations of wax and surface compounds 68 3.9 Relationships between wax and surface compounds and fruit characteristics 68 3.10 Do wax and surface compounds correlate with Monilia laxa infection probability? 69 4 Discussion 69 4.1 New compounds detected in fruit surface 70 4.2 Variations with cultivars and between years 71 4.3 Evolution of wax and surface compounds during development 71 4.4 Role of wax and surface compounds in preventing fruit gas exchanges 71 4.5 Potential effect of wax and surface compounds on brown rot infection 72 5 Conclusion 73 Chapitre 3: Exploration des caractéristiques physiques du fruit immature en relation avec la sensibilité à M. laxa 77 1 Introduction 78 2 Materials and methods 80 2.1 Vegetal material 80 2.2 Fruit sampling 80 2.3 Monilinia laxa 81 2.4 Infection tests 81 2.5 Fruit surface conductance assessment 82 2.6 Stomata number estimation 83 2.7 Genetic linkage map construction and QTL analysis 84 2.8 Projection of QTL on a physical map 85 2.9 Statistical analysis 85 3 Results 85 3.1 Physical characteristics of young fruit of the population 85 3.2 Infection probability 87 3.3 Links between fruits characteristics and fungal susceptibility 87 3.4 QTL location 88 4 Discussion 88 4.1 Marker density and population size – factors controlling QTL detection 88 4.2 Counting stomata number on a mapping population 89 4.3 Exploring the link between stomata number and conductance 90 4.4 Identification of loci governing surface conductance 91 4.6 Identification of loci governing infection probability and progression 92 4.7 Hypotheses to explain the variations in susceptibility of young peach to M. laxa 92 5 Conclusion 93 Chapter 4: Etude de la variabilité génétique et cartographie QTL de la résistance à la pourriture brune (Monilinia laxa) dans une descendance interspécifique issue d'un croisement entre Prunus persica et P. davidiana 97 1 Introduction 100 2 Materials and methods 102 2.1 Plant material 102 2.2 Monilinia laxa strain 103 2.3 Infection tests 103 2.4 Phenotyping 103 2.5 Measurements acquired in the laboratory test 104 2.6 Fruit surface conductance assessment 105 2.7 Genetic linkage map construction and QTL analysis 105 3 Results 106 3.1 Screening for brown rot resistance with infection tests 106 3.2 High variability of scoring between years 107 3.3 Natural infection of stems in spring 107 3.4 Natural infection of fruit in the orchard in 2015 107 3.5 Comparison between infection methodologies 107 3.6 Survey of infection progression through lab tests 108 3.7 Fruit surface conductance 108 3.8 QTL location 108 4 Discussion 109 4.1 The BC2 progeny: an interspecific back cross as a potential source of resistance to M. laxa 109 4.2 Infection tests for scoring brown rot resistance: with or without wounding fruit? 110 4.3 Infection tests for scoring brown rot resistance: drop or spray, orchard or lab, natural or artificial infections? 110 4.4 Trying to explain the high instability between years 112 4.5 The QTL for brow rot resistance: where are we now? 113 5 Conclusion 114 Chapter 5: Etude de la variabilité des composés d'épiderme des fuits d’ue desedae itespéifiue issue d'un croisement entre Prunus persica et P. davidiana et liens avec la susceptibilité à la pourriture brune 117 1 Materials and Methods 118 1.1 Fruit sampling 118 1.2 Epidermis preparation 118 1.3 Extraction 118 1.4 HPLC analyses 119 2 Results and discussion 120 2.1 Epidermis compounds showed great variations within the BC2 progeny 120 2.2 Some compounds were highly correlated between each other 120 2.3 Peaches and nectarines displayed huge differences 121 2.4 A hundred QTL were detected for epidermis compounds 121 2.5 Some compounds exhibited significant relationships with infection traits 122 2.6 Colocation of QTL for epidermis compounds and M. laxa susceptibility were observed 122 3 Conclusions 123 CONCLUSION GENERALE ET PERSPECTIVES 124 Coet phéotype la ésistae à la pouitue ue est pas ue uestion triviale 126 . ‘ésistae de lépidee et de la hai 126 1.2 Effet du bain-aie su la poailité difetio 126 . Coetatio e spoes de la suspesio difetio et volues déposés 127 . Goutte ou spay : uel test utilise ? 127 2 Facteurs de sensibilité et résistance à la pourriture brune: des progrès? 128 .
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